After that, upload it to your site via FTP, and run it (using your browser) as: http://yoursite.com/wordpress-fix.php

This script will take a few minutes to complete, but will scan your whole site and remove the malware entries.

Once you are done, go back to your site and remove this file.

That’s it and you should be clean again.

UPDATE: If your site is not getting cleanup after you run it (or you are getting extra empty lines on the top of your files), it means that the script didn’t finish to run properly. Try running it again. It it doesn’t help, upload it to some sub directories (like wp-admin, wp-content and wp-includes) and run directly from there. For example:
http://yoursite.com/wp-admin/wordpress-fix.php , http://yoursite.com/wp-content/wordpress-fix.php , etc.
That should fix it!